San Diego  Rising 16 stories above Broadway in the heart of downtown San Diego, the new federal courthouse annex took three years to build and cost $368 million.

It has 467,000 square feet of floor space, an underground garage and a tunnel linking the annex with the adjacent five-story Edward J. Schwartz courthouse just to the west.

What it doesn’t have is what federal judges and law enforcement said was most needed when the project was conceived a decade ago: more courtrooms for the San Diego federal court district.

In fact, when the annex becomes fully occupied and operational next year, there will be fewer federal courtrooms in San Diego than there were before a single shovel of dirt was turned on the annex project.

“When all is said and done,” said Chief Judge Barry Ted Moskowitz, “we’ll have two fewer courtrooms for $368 million.”

The reason lies in a resolution passed in September 2009 by the Committee on Transportation and Infrastructure of the U.S. House of Representatives. It approved the last $78 million needed to finish the project — but attached a number of conditions.

The resolution capped the total number of courtrooms in San Diego at 22 and required judges to share courtrooms.

Before construction, the Schwartz building had 24 courtrooms, and the annex added six courtrooms.

To comply with the congressional resolution’s limits, eight courtrooms now on the ground floor of the current courthouse will be eliminated and converted to offices for magistrate judges.

That makes 22 total courtrooms between the two building.

The new annex does have space with wiring, flooring and other infrastructure in place that can be converted for eight more courtrooms at some time in the future, Moskowitz said.

Having fewer courtrooms runs against the main reason given for more than a decade for building a new courthouse. Proponents noted that the San Diego federal court is annually among the nation’s busiest in terms of case filings and has 28 judges, including five on retired status and 10 magistrate judges.

In 2011, almost 6,000 criminal cases were filed in the court, an increase of more than 75 percent from those filed in 2006.

“The whole idea for the new courthouse was we needed more space to handle the huge number of border crimes cases the U.S. Attorney’s Office was filing,” Moskowitz said.

Rep. Susan Davis, a San Diego Democrat who worked to get the courthouse funded, said last week that members of the House infrastructure committee decided federal courts were overbuilt and lavish, and thought the San Diego project fit that description, too.

“They had a notion that the courthouses that had been built were too big, and had been given more space than they needed,” said Davis, who did not serve on the committee. “Their belief was there were ways of economizing on the space, and that’s how they would move forward. And the judges would have to work with that.”

The resolution also required space not in use for courtrooms or court-related activities be allocated to executive branch agencies and not the court. The court clerk’s offices and the court’s pretrial services agency are in the annex building, but much of the space is being used by the Internal Revenue Service and the U.S. Marshals Service.